seaview: init at 4.7 #46595

iimog · 2018-09-13T07:51:16Z

Motivation for this change

Add package for seaview, a GUI for molecular phylogeny

Things done

Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
Built on platform(s)
- NixOS
- macOS
- other Linux distributions
Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
Tested execution of all binary files (usually in ./result/bin/)
Determined the impact on package closure size (by running nix path-info -S before and after)
Fits CONTRIBUTING.md.

srhb · 2018-09-13T09:46:27Z

pkgs/applications/science/biology/seaview/default.nix

+
+  buildInputs = with pkgs; [ fltk libjpeg ];
+
+  patchPhase = "sed -i 's#PATH=/bin:/usr/bin#/usr/bin/env#' seaview.cxx";


Am I reading the source correctly that this is only used to get rm? And in that case, can you patch in the actual path from coreutils instead?

That's right it is just a single occurrence and only used to get rm working. In the next iteration I will follow your suggestion.

srhb · 2018-09-13T09:47:44Z

pkgs/applications/science/biology/seaview/default.nix

+  meta = with stdenv.lib; {
+    description = "GUI for molecular phylogeny";
+    longDescription = ''
+SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.


Would you mind indenting this? The multiline strings strip common leading whitespace just fine.

Not at all. Will indent in the next iteration.

srhb · 2018-09-13T09:48:34Z

pkgs/applications/science/biology/seaview/default.nix

@@ -0,0 +1,41 @@
+{ stdenv, fetchurl, pkgs }:


Please rely on the dependencies (like fltk and libjpeg) directly here, and get rid of the pkgs argument

Thanks for the comment.

srhb · 2018-09-13T10:06:46Z

@GrahamcOfBorg build seaview

GrahamcOfBorg · 2018-09-13T10:06:56Z

No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: seaview

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.

GrahamcOfBorg · 2018-09-13T10:07:23Z

Success on x86_64-linux (full log)

Attempted: seaview

Partial log (click to expand)

g++ -o seaview   seaview.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o resource.o nexus.o viewasprots.o racnuc_fetch.o concatenate.o statistics.o trees.o treedraw.o addbootstrap.o least_squares_brl.o pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o tbe.o Fl_Native_File_Chooser_FLTK.o raa_acnuc.o parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o  `fltk-config --use-images --ldflags` -ldl -lpthread -lz
installing
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/rgwwvypqy4fldyan3shxl1nbax58saz4-seaview-4.7
shrinking /nix/store/rgwwvypqy4fldyan3shxl1nbax58saz4-seaview-4.7/bin/seaview
strip is /nix/store/h0lbngpv6ln56hjj59i6l77vxq25flbz-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/rgwwvypqy4fldyan3shxl1nbax58saz4-seaview-4.7/bin
patching script interpreter paths in /nix/store/rgwwvypqy4fldyan3shxl1nbax58saz4-seaview-4.7
checking for references to /build in /nix/store/rgwwvypqy4fldyan3shxl1nbax58saz4-seaview-4.7...
/nix/store/rgwwvypqy4fldyan3shxl1nbax58saz4-seaview-4.7

GrahamcOfBorg · 2018-09-13T10:08:43Z

Success on aarch64-linux (full log)

Attempted: seaview

Partial log (click to expand)

g++ -o seaview   seaview.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o resource.o nexus.o viewasprots.o racnuc_fetch.o concatenate.o statistics.o trees.o treedraw.o addbootstrap.o least_squares_brl.o pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o tbe.o Fl_Native_File_Chooser_FLTK.o raa_acnuc.o parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o  `fltk-config --use-images --ldflags` -ldl -lpthread -lz
installing
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/q4xjdzrrjn0lbqa144adfmn4agp4rwfw-seaview-4.7
shrinking /nix/store/q4xjdzrrjn0lbqa144adfmn4agp4rwfw-seaview-4.7/bin/seaview
strip is /nix/store/y4ymnvgxygpq05h03kyzbj572zmh6zla-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/q4xjdzrrjn0lbqa144adfmn4agp4rwfw-seaview-4.7/bin
patching script interpreter paths in /nix/store/q4xjdzrrjn0lbqa144adfmn4agp4rwfw-seaview-4.7
checking for references to /build in /nix/store/q4xjdzrrjn0lbqa144adfmn4agp4rwfw-seaview-4.7...
/nix/store/q4xjdzrrjn0lbqa144adfmn4agp4rwfw-seaview-4.7

GrahamcOfBorg added 8.has: package (new) 10.rebuild-darwin: 0 10.rebuild-linux: 1-10 labels Sep 13, 2018

srhb requested changes Sep 13, 2018

View reviewed changes

seaview: init at 4.7

544ceb5

iimog force-pushed the init-seaview branch from 89824be to 544ceb5 Compare September 13, 2018 10:05

srhb approved these changes Sep 13, 2018

View reviewed changes

xeji merged commit e2df8e7 into NixOS:master Sep 13, 2018

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seaview: init at 4.7 #46595

seaview: init at 4.7 #46595

iimog commented Sep 13, 2018

srhb Sep 13, 2018

iimog Sep 13, 2018

srhb Sep 13, 2018

iimog Sep 13, 2018

srhb Sep 13, 2018

iimog Sep 13, 2018

srhb commented Sep 13, 2018

GrahamcOfBorg commented Sep 13, 2018

GrahamcOfBorg commented Sep 13, 2018

GrahamcOfBorg commented Sep 13, 2018


		buildInputs = with pkgs; [ fltk libjpeg ];

		patchPhase = "sed -i 's#PATH=/bin:/usr/bin#/usr/bin/env#' seaview.cxx";

seaview: init at 4.7 #46595

seaview: init at 4.7 #46595

Conversation

iimog commented Sep 13, 2018

Motivation for this change

Things done

srhb Sep 13, 2018

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iimog Sep 13, 2018

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srhb Sep 13, 2018

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iimog Sep 13, 2018

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srhb Sep 13, 2018

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iimog Sep 13, 2018

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srhb commented Sep 13, 2018

GrahamcOfBorg commented Sep 13, 2018

GrahamcOfBorg commented Sep 13, 2018

GrahamcOfBorg commented Sep 13, 2018